Problems I Have with the Bible

I know that it probably seems like heresy to some, but I do have some problems with the Bible. Now before you get too worked up with me, let me explain that I believe in the divine inspiration of the Bible. I believe that it is the word of God. Whenever I need to know God's will, be reminded of his way, or be refreshed by his words, I turn to the Bible. I own dozens of copies of the Bible. There are very few people I know who love the Bible more than I do.

That is why I have mixed emotions about what I am about to write. I love God and I love his word. I do not want to seem disrespectful, but there are some issues that I want to raise with the Almighty at the first opportunity. I have some questions that maybe only God can answer.

• The Prodigal Son (Luke 15). The story of the Lost Son is pretty straightforward and familiar to everyone. But I wonder about the older brother. He gets all the reward? His father insists that all he has belongs to the older brother. On the one hand this is only fair, but on the other, the father is to serve as a picture of God. Is this the loving Father that we are to believe in and hope for? When we turn from our sins can we anticipate forgiveness but no reward?
• The Wedding Feast (John 2). This was Jesus' first miracle- commonly referred to as turning water into wine. The servants in the story obeyed Jesus' directions to fill the jars with water. Why? No one had ever seen Jesus do a miracle, surely they did not expect one now. Why would they? Whose wedding was this? Why was Jesus so interested?
• Abraham and Isaac (Genesis 22). God called Abraham to sacrifice his son, Isaac. We know how the story turns out. We know that God provides a sacrifice in place of Isaac, but what a state of discomfort we go through on the way to the end of the story. Why does God do that? It seems like some sort of sick game that God is playing.
• Wrathful War. There are numerous instances in the Old Testament in which God orders his people to kill everyone of their enemies, including women and children. The Israelites, in fact, are punished when they do not completely kill everyone. Why would God order this? Isn't there a better way?